BRCA2 generic BayesDel threshold evidence-code assignment
Apply generic Pejaver thresholds to the same functional benign reference class; report BP4 coverage and erroneous PP3 assignment, not final classification accuracy.
Overview
Apply generic Pejaver thresholds to the same functional benign reference class; report BP4 coverage and erroneous PP3 assignment, not final classification accuracy.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
1 recorded evaluation, 2 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
1 evaluation · 2 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison | Protocol: BRCA2 generic BayesDel threshold evidence-code assignment Dataset: BRCA2 functional reference calibration set | <10% benign_reference_assigned_bp4 percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBRCA2 generic BayesDel threshold comparator Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Results, BayesDel calibration, BP4 code would be assigned to <10% of BRCA1 and BRCA2 benign reference variants |
| Configuration: BayesDel generic Pejaver evidence thresholds in ENIGMA comparison | Protocol: BRCA2 generic BayesDel threshold evidence-code assignment Dataset: BRCA2 functional reference calibration set | 36% benign_reference_assigned_pp3 percent · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceBRCA2 generic BayesDel threshold comparator Not reported Aggregation: Not reported Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Results, BayesDel calibration, sentence 29% for BRCA1 and 36% for BRCA2 incorrectly assigned PP3 |
Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
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Recorded evaluations
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Baseline coverage
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0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 1
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Training-set class prior where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Regularised classifier on simple permitted features, or protocol's conventional reference
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-30-e37e3ab1284d. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Applicable tests and references
Applicability is distinct from a completed evaluation.
- Generic BayesDel computational-evidence threshold baseline · source_supported
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of uc-clinical-20260930-benchmark-enigma-study Individual claims | Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel Table2; calibration Results; pilot curation Version: 2024 final article; reported VCEP specifications v1.0 | source checked automated source review · 2026-09-30 Audit detailsTranscription from inspected primary source. No execution, independent replication or human scientific review. Field: Claim: uc-clinical-20260930-membership-enigma-brca2-generic-protocol Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-30-e37e3ab1284d · Record review: source checked
1 source records and release history
- Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel · Original source · 2024 final article; reported VCEP specifications v1.0
Technical metadata and extraction receipts
Stable ID: uc-clinical-20260930-enigma-brca2-generic-protocol
- areas
- dna-genomes
- contexts
- clinical_research
- protocol
- Apply generic Pejaver thresholds to the same functional benign reference class; report BP4 coverage and erroneous PP3 assignment, not final classification accuracy.
- review
- method: automated_source_review; reviewer: Codex clinical coverage worker; date: 2026-09-30; note: Transcription from inspected primary source. No execution, independent replication or human scientific review.; source id: uc-clinical-20260930-source-enigma
- limitations
- Functional proxy labels, not independent clinical classifications.; Primary narrative only; complete Supplementary Table S4 unavailable.